Overview

Augustin Luna
09 January, 2016

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

Topics to be Covered

  • R: Language Basics, Plotting, Getting Help
  • Using the RStudio Editor
  • Machine Learning Fundamentals
    • Dimension Reduction
    • Regression
    • Clustering
  • Accessing Datasets: CellMiner (cell lines/drugs), CBioPortal (patient samples), Pathway Commons (pathways)
  • Developing Web Applications

What is R?

  • Free, open source
  • Started in 1993
  • Geared towards scientific computing
    • Created by Ross Ihaka and Robert Gentleman (statisticians)
  • Interpreted; similar to Python and MATLAB

Why is R Popular?

  • Free, open source
  • Interactive data analysis
    • Script-driven rather than menu-driven helps reproducibility
  • Flexible and powerful plotting support
  • Excellent package management system
    • Large and growing collection of statistical analysis methods
    • Simple package installation; dependency management
    • R scripts usually portable to other platforms
    • Package repositories ensure functionality, documentation, and interoperability
    • Vignettes (tutorials) provided as runnable analyses

Extending R and Package Repositories

  • Comprehensive R Archive Network (CRAN)
    • 5,800 R packages (as of June 2014)
    • Many packages call C, C++, Fortran, or Java code for speedups
  • Bioconductor
    • 800+ R packages focused on bioinformatics
    • 50+ packages dedicated to pathway analysis
  • Devtools
    • R package that allows package installation from code repositories

RStudio

  • https://www.rstudio.com/
  • Available for Windows, OSX, and Linux
  • Simplifies common tasks: plotting, package installation, accessing files, viewing variables, etc.

Installing R and RStudio

RStudio Overview

Editor
Environment
Plot
Console

Table View of Variables

  • Highlighted boxes open a table view of variable contents

Change Current Directory

  • Highlighted boxes open a table view of variable contents

Making a New R Script

First Script: Hello World!

  • cat() prints a simple message in the console
cat("Hello World!")

Hello World!

Running Hello World Script

  • “Run” button runs current line or selected lines
  • “Source” button runs all lines in file

Installing Packages

  • CRAN packages can be installed using RStudio or install.packages()